14 variations found. Os08g0511000/LOC_Os08g40020 (selenium binding protein; putative; expressed), ranging from 25,344,704 bp to 25,346,660 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os08g40020 | selenium binding protein, putative, expressed; RAP ID: Os08g0511000; MSU ID: LOC_Os08g40020 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg0825344877 (J) | chr08 | 25344877 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os08g40020.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os08g40010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.233; most accessible tissue: Zhenshan97 flag leaf, score: 94.214 |
| vg0825345259 (J) | chr08 | 25345259 | G | A | 85.20% | 0.00% | G -> A |
LOC_Os08g40020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.005; most accessible tissue: Zhenshan97 flag leaf, score: 93.782 |
|
| vg0825345472 (J) | chr08 | 25345472 | G | A | 90.30% | 0.00% | G -> A | NA |
LOC_Os08g40020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 86.091; most accessible tissue: Zhenshan97 flag leaf, score: 90.996 |
| vg0825345516 (J) | chr08 | 25345516 | C | T | 93.10% | 0.00% | T -> C | NA |
LOC_Os08g40020.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.475; most accessible tissue: Zhenshan97 flag leaf, score: 90.577 |
| vg0825345546 (J) | chr08 | 25345546 | C | T | 96.40% | 0.00% | C -> T |
LOC_Os08g40020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 85.404; most accessible tissue: Zhenshan97 flag leaf, score: 90.842 |
|
| vg0825345627 (J) | chr08 | 25345627 | C | T | 94.90% | 0.00% | C -> T |
LOC_Os08g40020.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 77.873; most accessible tissue: Zhenshan97 young leaf, score: 87.993 |
|
| vg0825345819 (J) | chr08 | 25345819 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os08g40020.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 64.827; most accessible tissue: Callus, score: 86.972 |
| vg0825346100 (J) | chr08 | 25346100 | G | A | 94.90% | 0.00% | G -> A |
LOC_Os08g40020.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 62.299; most accessible tissue: Callus, score: 69.474 |
|
| vg0825346286 (J) | chr08 | 25346286 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os08g40020.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)
LOC_Os08g40010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 49.552; most accessible tissue: Callus, score: 85.682 |
| vg0825346328 (J) | chr08 | 25346328 | T | G | 54.60% | 0.06% | G -> T |
mr1212 (All); LR P-value: 4.92E-06;
mr1446 (All); LR P-value: 2.39E-08; mr1518 (Jap_All); LR P-value: 2.63E-06; mr1727 (All); LR P-value: 7.02E-06; mr1746 (All); LR P-value: 3.25E-10; mr1989 (All); LR P-value: 1.60E-07; mr1730_2 (Jap_All); LR P-value: 6.77E-07; mr1866_2 (Jap_All); LR P-value: 4.35E-06; mr1885_2 (All); LR P-value: 2.16E-07 |
LOC_Os08g40020.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40010.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 42.571; most accessible tissue: Callus, score: 60.213 |
| vg0825346415 (J) | chr08 | 25346415 | T | C | 80.90% | 0.00% | T -> C |
LOC_Os08g40020.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40010.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 41.207; most accessible tissue: Callus, score: 60.213 |
|
| vg0825346438 (J) | chr08 | 25346438 | A | G | 99.20% | 0.00% | A -> G | NA |
LOC_Os08g40020.1 Alt: G| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os08g40010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 43.047; most accessible tissue: Callus, score: 83.528 |
| vg0825346493 (J) | chr08 | 25346493 | A | G | 85.10% | 0.00% | A -> G |
LOC_Os08g40010.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40020.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 38.736; most accessible tissue: Callus, score: 83.528 |
|
| vg0825346640 (J) | chr08 | 25346640 | T | A | 85.10% | 0.00% | T -> A |
LOC_Os08g40020.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os08g40010.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os08g40030.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 42.353; most accessible tissue: Callus, score: 63.595 |